You can create a new translation memory in Trados Workbench. Then import the txt file resulting from WinAlign (File > Import and select tmx as file type). After the importing process, you can export the translation memory into tmx selecting File > Export.

Oscar

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TMX is surely better than trados importable txt for widespread use as it is compatible with more CAT tools.

1000 files is a lot, so you may want to merge files and create one file and one TM for each specialization/area. Aligning 10 files (or 1) is a lot less hassle than aligning the same material in 1000 files, and the same applies to managing said TMs after alignment.

If you have lots of aligned TMs in trados txt format already, you could merge them, remove the unneeded headers and convert the whole thing to TMX together. (But your post is unclear about whether you've done the alignment or you just have the source files at this point, which should be in txt.)

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